Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
A searchable table of the S. cerevisiae pangenome ORFs defined in Peter et al. (2018) Nature (LINK) is provided below. The listed core/accessory classification and origin assignment are based on the original study. Click on the PanORF ID to find out the detailed presence/absence pattern of the corresponding pangenome ORF in both ScRAPdb and the 1002ScGP strain collections (which were recalculated by ScRAPdb).
| PanORF ID | SGD systematic Name | SGD standard name | Alias | Description | Type | Origin assignment | Mostly likely origin species | NCBI megablast hit |
|---|---|---|---|---|---|---|---|---|
| 4883-YJL189W_NumOfGenes_2 | YJL189W | RPL39 | eL39|ribosomal 60S subunit protein L39|L39e|YL40|L46|L39|SPB2|RPL46 | Ribosomal 60S subunit protein L39; required for ribosome biogenesis; loss of both Rpl31p and Rpl39p confers lethality; also exhibits genetic interactions with SIS1 and PAB1; homologous to mammalian ribosomal protein L39, no bacterial homolog | Core | NA | NA | NA |
| 4884-YJL190C | YJL190C | RPS22A | uS8|ribosomal 40S subunit protein S22A|S8|rp50|YS22|S24A|S22A|RPS24 | Protein component of the small (40S) ribosomal subunit; homologous to mammalian ribosomal protein S15A and bacterial S8; RPS22A has a paralog, RPS22B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4885-YJL191W | YJL191W | RPS14B | uS11|ribosomal 40S subunit protein S14B|S11|rp59B|S14B|CRY2 | Protein component of the small (40S) ribosomal subunit; required for ribosome assembly and 20S pre-rRNA processing; mutations confer cryptopleurine resistance; homologous to mammalian ribosomal protein S14 and bacterial S11; RPS14B has a paralog, RPS14A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4886-YJL192C | YJL192C | SOP4 | EMC7 | ER-membrane protein; subunit of evolutionarily conserved EMC (Endoplasmic Reticulum Membrane Complex) implicated in ERAD (ER-associated degradation) and proper assembly of multi-pass transmembrane (TM) proteins; EMC acts in yeast as an ER-mitochondria tether that interacts with outer membrane protein Tom5 of TOM (Translocase of the Mitochondrial Outer Membrane) complex; suppressor of pma1-7, deletion of SOP4 slows down export of wild-type Pma1p and Pma1-7 from the ER | Core | NA | NA | NA |
| 4887-YJL193W | YJL193W | NA | NA | Putative protein of unknown function; predicted to encode a triose phosphate transporter subfamily member based on phylogenetic analysis; similar to YOR307C/SLY41; deletion mutant has a respiratory growth defect | Core | NA | NA | NA |
| 4888-YJL194W_NumOfGenes_2 | YJL194W | CDC6 | AAA family ATPase CDC6 | Essential ATP-binding protein required for DNA replication; component of the pre-replicative complex (pre-RC) which requires ORC to associate with chromatin and is in turn required for Mcm2-7p DNA association; homologous to S. pombe Cdc18p; relocalizes from nucleus to cytoplasm upon DNA replication stress; degraded in response to plasma membrane stress | Core | NA | NA | NA |
| 4889-YJL196C | YJL196C | ELO1 | fatty acid elongase ELO1 | Elongase I, medium-chain acyl elongase; catalyzes carboxy-terminal elongation of unsaturated C12-C16 fatty acyl-CoAs to C16-C18 fatty acids; ELO1 has a paralog, ELO2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4890-YJL197W_NumOfGenes_2 | YJL197W | UBP12 | putative ubiquitin-specific protease UBP12 | Ubiquitin-specific protease; cleaves ubiquitin from ubiquitinated proteins; present in the nucleus and cytoplasm | Core | NA | NA | NA |
| 4891-YJL198W | YJL198W | PHO90 | SPX domain-containing inorganic phosphate transporter | Low-affinity phosphate transporter; acts upstream of Pho81p in regulation of the PHO pathway; deletion of pho84, pho87, pho89, pho90, and pho91 causes synthetic lethality; transcription independent of Pi and Pho4p activity; overexpression results in vigorous growth; PHO90 has a paralog, PHO87, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4892-YJL199C | YJL199C | MBB1 | NA | Putative protein of unknown function; conserved among S. cerevisiae strains, not conserved in closely related Saccharomyces species; protein detected in large-scale protein-protein interaction studies; YJL199C is not an essential gene | Core | NA | NA | NA |
| 4893-YJL200C | YJL200C | ACO2 | aconitate hydratase ACO2 | Putative mitochondrial aconitase isozyme; similarity to Aco1p, an aconitase required for the TCA cycle; expression induced during growth on glucose, by amino acid starvation via Gcn4p, and repressed on ethanol | Core | NA | NA | NA |
| 4894-YJL201W | YJL201W | ECM25 | NA | Non-essential protein of unknown function; promoter contains a consensus binding sequence for factor Abf1p | Core | NA | NA | NA |
| 4895-YJL202C | YJL202C | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps 3' end of essential PRP21 gene encoding a subunit of the SF3a splicing factor complex | Accessory | Ancestral | NA | NA |
| 4896-YJL203W | YJL203W | PRP21 | SPP91 | Subunit of the SF3a splicing factor complex; required for spliceosome assembly | Core | NA | NA | NA |
| 4897-YJL204C | YJL204C | RCY1 | NA | F-box protein involved in recycling endocytosed proteins; involved in recycling plasma membrane proteins internalized by endocytosis; localized to sites of polarized growth; direct interaction with C-terminal cytoplasmic region of Drs2p plays an important role for Drs2p function in endocytic recycling pathway | Core | NA | NA | NA |